Drug addiction is a complex disorder thought to involve the interaction of environmental factors with multiple genetic factors. Combinations of genetic variations in several genes likely cooperate to increase the susceptibility of an individual to addiction. Candidate genes are those encoding drug metabolizing enzymes and transporters, neurotransmitter receptors, signaling proteins, and proteins affecting neurobiological functions, such as synaptic remodeling and memory. Polymorphisms that alter protein structure have been studied extensively, but cis-acting variations affecting gene expression and mRNA processing are likely to be more prevalent. Therefore, cis-regulatory polymorphisms might account for much of the diversity between individuals and their susceptibility to addiction. Yet, it has proven difficult to detect such cis-regulatory variants across a large panel of genes. Here, a novel approach to screen broadly for polymorphisms that affect gene expression and mRNA processing is introduced, taking advantage of single nucleotide polymorphisms (SNPs) in the transcribed region of a candidate gene. By precisely measuring the ratios of the two SNP alleles in both genomic DNA and mRNA in heterozygous carriers, one detects variations in mRNA levels, comparing one allele against the other in a relevant target tissue obtained by autopsy from multiple individuals. Genes showing significant allelic differences in mRNA levels are scanned for functional polymorphisms by haplotype and association analysis. The specific aims of this study are to: 1) Identify candidate genes with suitable marker SNPs located in transcribed regions that exhibit allele-specific mRNA differences in relevant target tissues (e.g., brain regions, liver). 2) Isolate haplotype blocks that are associated with differential allelic expression. 3) Discover functional genetic lesions associated with differential allelic expression. The results will permit us to assign functional significance to cis-regulatory polymorphisms as a guide in clinical association studies of drug addiction.